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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 490c0509fbaaacd763091baf3e1ebdf0b69a829e
author iuc
date Thu, 26 Sep 2024 15:27:06 +0000
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-1:000000000000 0:b6e65b5074c0
1 <?xml version="1.0"?>
2 <tool id="tsebra" name="TSEBRA" version="@TOOL_VERSION@+galaxy0" profile="21.05">
3 <description>tanscript selector for BRAKER</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">tsebra</xref>
9 </xrefs>
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14 tsebra.py
15
16 #if str( $gtf_file_param ) == "GTF":
17 -g '$gtf_input'
18 #elif str( $gtf_file_param ) == "KEEP_GTF":
19 -k '$gtf_input'
20 #end if
21
22 #if $hint_file
23 -e '$hint_file'
24 #end if
25 #if $cfg_file
26 -c '$cfg_file'
27 #end if
28
29 $ignore_tx_phase
30 #if $filter_exon
31 --filter_single_exon_genes
32 #end if
33 #if $score_tab
34 --score_tab '$output_tab'
35 #end if
36
37 -o '$output'
38 ]]></command>
39 <inputs>
40 <param name="gtf_input" type="data" format="gtf" label="GTF input"/>
41 <param name="gtf_file_param" type="select" label="Choose the analysis parameter for the gtf file">
42 <option value="GTF" selected="true">List of gene prediciton files</option>
43 <option value="KEEP_GTF">All transcripts from these gene sets will be included in the output</option>
44 </param>
45 <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/>
46 <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/>
47 <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
48 <param name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
49 <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/>
50 <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
51 </inputs>
52
53 <outputs>
54 <data name="output" format="gtf" label="TSEBRA on ${on_string}"/>
55 <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab">
56 <actions>
57 <action name="column_names" type="metadata" default="TX_ID,intron_support,stasto_support,s1,s2,s3,s4" />
58 </actions>
59 <filter>score_tab</filter>
60 </data>
61 </outputs>
62
63 <tests>
64 <test expect_num_outputs="1">
65 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
66 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
67 <param name="score_tab" value="false"/>
68 <param name="gtf_file_param" value="GTF"/>
69 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
70 </test>
71
72 <test expect_num_outputs="2">
73 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
74 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
75 <param name="score_tab" value="true"/>
76 <param name="gtf_file_param" value="GTF"/>
77 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
78 <output name="output_tab" ftype="txt">
79 <assert_contents>
80 <has_size value="32000" delta="300"/>
81 <has_text text="anno1;g1.t1"/>
82 <has_text text="anno1;g59.t1"/>
83 <has_text text="anno1;g169.t1"/>
84 </assert_contents>
85 </output>
86 </test>
87 </tests>
88
89 <help><![CDATA[
90 tsebra_ TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence
91 in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions.
92
93
94 .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA
95 ]]></help>
96 <expand macro="citation"></expand>
97 </tool>